Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,894,650	G→A	6.9%	G89E (GGG→GAG)	PP_2549 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,894,650	0	G	A	6.9%	167.3 / 3.1	58	G89E (GGG→GAG)	PP_2549	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (32/22);  new base A (2/2);  total (34/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

GGCGCTGATGCTCAAGGAAGCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGCCCAGGTCGGT  >  NC_002947/2894507‑2894792                                                                                                                                                 |                                                                                                                                               ggCGCTGATGCTCAAGGAAGCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGc                                                                                                                                          >  1:63560/1‑150 (MQ=255)        aTGCTCAAGGAAGCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCg                                                                                                                                   >  2:1403329/1‑150 (MQ=255)               aGGAAGCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGa                                                                                                                                       >  1:743424/1‑139 (MQ=255)               aGGAAGCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGa                                                                                                                                       <  2:743424/139‑1 (MQ=255)                    gCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGg                                                                                                                                               <  1:1259274‑M2/126‑2 (MQ=255)                    gCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGg                                                                                                                                               >  2:1259274‑M2/1‑125 (MQ=255)                        tACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTAATTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTg                                                                                                                   >  2:209143/1‑150 (MQ=255)                          ccGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAg                                                                                                                 >  1:807880/1‑150 (MQ=255)                              aacTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCgg                                                                                                             >  1:630692/3‑150 (MQ=255)                                          tgCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCATTCTCGGAC‑GTCTGTTCGGGGGGGCGGAGGCGGTGCGGCTTGTGCGTGAGTCGGAGCGCAGCATTa                                                                                                 >  2:161727/1‑150 (MQ=255)                                          tgCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTa                                                                                                 >  2:127650/1‑150 (MQ=255)                                             tGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAg                                                                                              >  2:835145/1‑150 (MQ=255)                                                   aGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCg                                                                                        <  2:630692/150‑1 (MQ=255)                                                   aGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCCCGAACAGGC‑GTTCGAgggtgaagtacttggcc                                                                                                                               >  2:27309‑M2/1‑94 (MQ=255)                                                   aGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCCCGAAC‑AGGCGTTCGAgggtgaagtacttggcc                                                                                                                               <  1:27309‑M2/111‑18 (MQ=255)                                                     tccaaCATCTTTGTTGCCGGTGCCAGCGGCCGCAATGGGGGCTTTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTGGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCggg                                                                                      <  2:632173/146‑1 (MQ=255)                                                     gCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCggg                                                                                      <  1:1013011/150‑1 (MQ=255)                                                     gCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAAAAGAGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCggg                                                                                      <  1:653874/150‑1 (MQ=255)                                                      ccGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGCAGCGCAGCATTACAGCCACTgggg                                                                                     <  2:799014/150‑1 (MQ=255)                                                      ccGACATCTGTGGTACCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAg                                                                                                                                      >  1:460595/1‑101 (MQ=255)                                                      ccGACATCTGTGGTACCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAg                                                                                                                                      <  2:460595/101‑1 (MQ=255)                                                       cGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCggggg                                                                                    >  1:632173/1‑149 (MQ=255)                                                       cGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGgt                                                                                    >  2:30111/1‑150 (MQ=255)                                                       cGACATAGGTGGTGCCGGTGCCCGCGGCCGCACTGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCCGTTCGGGGCGCCGCAAGCGGTACGGCTGGTGCGGGAGACGTCGCGCAGCATCAACGACAGCGGGgt                                                                                    >  2:640445/1‑150 (MQ=255)                                                        gACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCTAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGAGGGAGTCGGAGCGCAGCATTACAGACATCGGGgtg                                                                                   <  1:824711/150‑1 (MQ=255)                                                        gACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCgggggg                                                                                   >  1:951961/1‑148 (MQ=255)                                                         tcacccgtggtgCCGGTGCCAGCGGCCGCCATGGGGCCTGCGCGTTGTCCTGGTCGGCTAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGTCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGgtgt                                                                                  <  2:234397/144‑1 (MQ=255)                                                         aCATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGgtgt                                                                                  >  2:710849/1‑150 (MQ=255)                                                                tggtgCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTgcgc                                                                           <  1:835145/150‑1 (MQ=255)                                                                       ggtgccAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAAt                                                                    <  2:807880/150‑1 (MQ=255)                                                                        gagccAGCGGCCGCAATGGGGGCTGTGTGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATg                                                                   <  2:705508/148‑1 (MQ=255)                                                                             aGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATc                                                              >  2:1163724/1‑150 (MQ=255)                                                                                ggCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCgg                                                                         <  1:97128/136‑1 (MQ=255)                                                                                ggCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCgg                                                                         >  2:97128/1‑136 (MQ=255)                                                                                                          cTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGa                                                                                                                  >  2:25799/1‑69 (MQ=255)                                                                                                          cTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGa                                                                                                                  <  1:25799/69‑1 (MQ=255)                                                                                                           tGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTg                                >  2:236702/1‑150 (MQ=255)                                                                                                                ggCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTacac                           >  1:144992/1‑150 (MQ=255)                                                                                                                  ccAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACgg                         >  1:370169/1‑150 (MQ=255)                                                                                                                      gTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGccac                     <  1:1403329/150‑1 (MQ=255)                                                                                                                         cTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCaa                  >  1:1025109/1‑150 (MQ=255)                                                                                                                            cACCCTCGAAC‑GCCTGTTCGGgggtgaagtacttggccgaccaggacaacgcacagcccccattgcggccgctggcaccggcaccacagatgtcggcctcgatcagcaccacatccagggccggtaccgcttccttgagcatcagcgccg               <  1:1381354‑M2/150‑130 (MQ=255)                                                                                                                              cccTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAg             <  1:30111/150‑1 (MQ=255)                                                                                                                               ccTCGAAC‑GCCTGTTCGGgggtgaagtacttggccgaccagga                                                                                                                       <  1:927462‑M2/43‑26 (MQ=255)                                                                                                                               ccTCGAAC‑GCCTGTTCGGgggtgaagtacttggccgaccagga                                                                                                                       >  2:927462‑M2/1‑18 (MQ=255)                                                                                                                               ccTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGt                                                                                                                    >  1:1111154/1‑46 (MQ=255)                                                                                                                               ccTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGt                                                                                                                    <  2:1111154/46‑1 (MQ=255)                                                                                                                               ccTCGAAC‑GCCTGTTCGAgggtgaagtacttggccgaccaggacaacgcacagcccccattgcggccgctggcaccggcac                                                                                 >  2:77936‑M2/1‑18 (MQ=255)                                                                                                                               ccTCGAAC‑GCCTGTTCGAgggtgaagtacttggccgaccaggacaacgcacagcccccattgcggccgctggcaccggcac                                                                                 <  1:77936‑M2/81‑64 (MQ=255)                                                                                                                                 tCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGccc          >  1:17316/1‑150 (MQ=255)                                                                                                                                 tCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGccc          >  1:161842/1‑150 (MQ=255)                                                                                                                                 tCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACCGCCACCAACGCAGccc          >  2:461686/1‑150 (MQ=255)                                                                                                                                  cGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGCCCa         <  1:209143/150‑1 (MQ=255)                                                                                                                                    aaC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGCCCAgg       >  1:129388/1‑150 (MQ=255)                                                                                                                                         ccTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATGACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGCCCAGGTCgg   >  1:36292/1‑150 (MQ=255)                                                                                                                                          cTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGTGCCGGCCCGCCGGATTGCAGCGATCATGCTGAGATCCCTGGGGTAGATGATGTACATCGACTTCCGCCTGGTCGGCACGCTGTACACGGCCACCAACGCAGCCCAGGTCGGt  >  2:872336/1‑150 (MQ=255)                                                                                                                                             ttCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGCCCAGGTCGGt  >  1:255730/1‑147 (MQ=255)                                                                                                                                             ttCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGCCCAGGTCGGt  <  2:255730/147‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                               GGCGCTGATGCTCAAGGAAGCGGTACCGGCCCTGGATGTGGTGCTGATCGAGGCCGACATCTGTGGTGCCGGTGCCAGCGGCCGCAATGGGGGCTGTGCGTTGTCCTGGTCGGCCAAGTACTTCACCCTCGAAC‑GCCTGTTCGGGGGGGCGGAGGCGGTGCGGCTGGTGCGTGAGTCGGAGCGCAGCATTACAGACATCGGGGTGTTCTGCGCGGCCAATGGCATCGACTGCGACTTCCGCCTGGACGGCACGCTGTACACGGCCACCAACGCAGCCCAGGTCGGT  >  NC_002947/2894507‑2894792

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑